Timeline


and

10/12/07:

16:42 Ticket #198 (OME-TIFF files fail with Bio-Formats Importer plugin) created by curtis
When importing OME-TIFF files to ImageJ using the Bio-Formats Importer …
16:40 Ticket #197 (Bio-Formats Importer fails with indexed images) created by curtis
Attempting to import an indexed color image with the Bio-Formats Importer …
15:56 Ticket #196 (ZVI reader sometimes reverses Z and T dimensions) created by curtis
The dataset in data/zeiss-zvi/monica/Monica_elegans_movie.zvi has 14 …
15:30 Changeset [3273] by curtis
Fix little bug in arg parsing.
13:04 Changeset [3272] by melissa
More tiling/BigTIFF fixes.
11:33 Changeset [3271] by melissa
Corrected image count calculation if we have indexed color planes.
09:03 Ticket #158 (Add support for BigTiff) closed by melissa
fixed: Complete in r3270.
08:46 Changeset [3270] by melissa
Fixed tiling bug and added remaining BigTIFF types.

10/11/07:

15:17 Changeset [3269] by melissa
Initial implementation of BigTIFF.
14:32 Changeset [3268] by melissa
Removed several hacks that added an extra blank channel if C == 2.
14:31 Ticket #195 (Cannot construct 2-channel images with ImageTools) closed by melissa
fixed: Fixed in r3267. Solution was to add new 2-component ColorSpace …
13:45 Changeset [3267] by melissa
Added new ColorSpace for 2-channel images; updated ImageTools accordingly.
12:46 Changeset [3266] by melissa
Fixed plane number -> IFD mapping for primary file.
12:23 Changeset [3265] by curtis
Clean up and debug image construction methods.
12:22 Changeset [3264] by curtis
Use BYTES_PER_ENTRY instead of hardcoded 12 where relevant.
12:20 Changeset [3263] by curtis
Rename "used" to "usedFiles" so it is easier to search.
10:51 Changeset [3262] by curtis
Remove unnecessary imports.
09:49 Changeset [3261] by melissa
Only parse the primary file once.
09:26 Changeset [3260] by curtis
TiffComment now has a trivial implementation thanks to …
09:17 Changeset [3259] by curtis
* Add TiffTools.getComment convenience method. * Some efficiency …
08:27 Changeset [3258] by melissa
Removed option to force compatible pixel type.

10/10/07:

17:26 Changeset [3257] by curtis
Standardize getPixels methods to use a single sample model checker method …
17:23 Ticket #195 (Cannot construct 2-channel images with ImageTools) created by curtis
Currently, ImageTools throws an exception when you attempt to create a …
15:12 Changeset [3256] by curtis
Comment out reference to broken makeType method.
15:10 Changeset [3255] by curtis
Comment out reference to broken makeType method.
15:09 Changeset [3254] by curtis
Fix getPixels implementations to never use makeType, and get rid of …
13:52 Ticket #170 (Investigate ImageJ's VirtualStack objects) closed by melissa
fixed: In order to create a VirtualStack, each plane of the dataset must be …
12:33 Ticket #175 (More cohesive floating point image support) closed by melissa
fixed: As of r3253, all byte array to float array conversions are done using …
12:24 Changeset [3253] by melissa
All byte array to float array conversions are now handled by …
11:19 Changeset [3252] by melissa
Fixed bug in fake rows per strip calculation.
10:54 Ticket #192 (Default implementation for saveBytes) closed by melissa
fixed: Completed in r3251. In order to use saveBytes, a valid MetadataRetrieve …
10:52 Changeset [3251] by melissa
Added default saveBytes implementations. To use saveBytes, a …

10/09/07:

23:58 Ticket #194 (Investigate usage of JMF library) created by curtis
The [ http://java.sun.com/products/java-media/jmf/index.jsp Java Media …
15:06 Changeset [3250] by curtis
Disable editing of file path text boxes for now.
15:04 Ticket #193 (Test omeul with OME 2.6.1) created by curtis
The client-side OME upload functionality provided by the omeul script has …
14:35 Changeset [3249] by melissa
Fixed pixel type mismatch.
14:06 Ticket #192 (Default implementation for saveBytes) created by curtis
Adding a default implementation for the FormatWriter.saveBytes methods …
13:57 Changeset [3248] by melissa
Fixed series/currentSeries typo; update file map along with IFD map.
13:39 Ticket #159 (Add support for compressed ZVI images) closed by melissa
fixed: Finished in r3247.
13:38 Changeset [3247] by melissa
Added support for JPEG-compressed ZVI images.
13:17 Changeset [3246] by melissa
Fixed one last bug.
12:55 Changeset [3245] by melissa
Parse XML using SAX.
11:16 Ticket #191 (3-view) created by curtis
(From Matt Conklin) It may be useful to generate a "3-view" of the plot. …
11:16 Ticket #190 (Export to spreadsheet) created by curtis
(From Matt Conklin) It would be great to get the data seamlessly into a …
11:15 Ticket #189 (Save/export to figure file) created by curtis
(From Matt Conklin) Saving/exporting the plot into a figure making …
11:15 Ticket #188 (Overlapping line and surface plots) created by curtis
(From Matt Conklin) Overlapping the line plots of the data over the …
10:40 Ticket #187 (Model some data for testing) created by curtis
To verify the accuracy and proper behavior of Slim Plotter's algorithms, …
10:38 Ticket #186 (Plot chi-squared error graphically) created by curtis
It is currently possible to plot the exponential curve fit results …
10:26 Ticket #185 (Plot system response data graphically) created by curtis
To give the user a better idea of exactly what is being done by the …
10:20 Ticket #184 (Additional logic for handling background issues) created by curtis
When fitting exponential curves, the c value represents the background. …
09:51 Ticket #183 (Devise a scheme to embed calibration information into the SDT format) created by curtis
As mentioned in tickets #84 and #135, we need to embed calibration …

10/08/07:

14:02 Ticket #176 (ImageJ stack ordering broken) closed by melissa
fixed: Fixed in r3244.
13:58 Changeset [3244] by melissa
Added option to open each plane in a separate window; fixed CustomImage …
12:27 Changeset [3243] by curtis
Echo status message events to the ImageJ status bar.
12:18 Changeset [3242] by curtis
Add Javadoc for getReorderedIndex.
12:14 Changeset [3241] by curtis
Another status message, indicating parsing of each constituent OME-TIFF …
12:08 Changeset [3240] by curtis
Add status message for each TIFF file checked.
12:08 Ticket #182 (Fix bug with >2GB LIF files) closed by melissa
fixed: Fixed in r3239.
12:07 Changeset [3239] by melissa
Fixed bug with >2GB files.
11:56 Ticket #182 (Fix bug with >2GB LIF files) created by melissa
Leica LIF files larger than 2GB throw the following exception: […]
11:53 Changeset [3238] by melissa
Improved logic for mapping plane numbers to IFDs - scrambled TiffData …
11:38 Ticket #171 (Improve OME-TIFF grouping logic) closed by curtis
fixed: Melissa has improved the OME-TIFF reader's file grouping logic and fixed …
11:34 Ticket #181 (Investigate LSM data with nonstandard LZW compression) created by curtis
The LSM files in data/zeiss-lsm/tom have problems being decoded properly …
11:25 Ticket #180 (AVI codecs supported by NIS Elements) created by melissa
The following AVI codecs are supported by NIS Elements: * Cinepak * …
11:24 Ticket #179 (Add support for compressed LIM files) created by melissa
Pixels in a LIM file can be compressed using a proprietary lossless …
11:22 Ticket #178 (Add support for Imaris 5.5) created by melissa
Need to obtain sample data by installing latest Imaris version; add …
11:18 Ticket #177 (Additional plugin options) created by melissa
Two new ImageJ plugin features have been requested: 1. Open each plane …
11:13 Ticket #176 (ImageJ stack ordering broken) created by melissa
When other options (e.g. "merge channels to RGB") are checked, the …
10:54 Ticket #175 (More cohesive floating point image support) created by curtis
Currently Bio-Formats has duplicate implementations of byte-array-to-float …
10:44 Ticket #174 (Investigate usage of Sanselan image library) created by curtis
A new pure Java image library has recently been released called …
10:40 Ticket #173 (Standard way to "fail through" to another reader) created by curtis
In some cases, there are multiple readers that can ostensibly support a …
10:32 Ticket #172 (Better usage of JAI Image I/O Tools) created by curtis
Bio-Formats currently uses the [ https://jai-imageio.dev.java.net/ JAI …
10:06 Changeset [3237] by melissa
Fixed sizeC calculation for RGBA TIFFs.

10/05/07:

19:23 Changeset [3236] by curtis
Use openmicroscopy.org, not org.openmicroscopy, for IDs.
15:33 Changeset [3235] by curtis
Fix typo in Pixels IDs.
15:19 Changeset [3234] by curtis
Brief what's new for minor 2007 Oct 5 Bio-Formats release.
14:55 Changeset [3233] by curtis
Fix bug with scramble feature.
14:43 Changeset [3232] by curtis
Fix multi-Image and multi-Pixels TiffData tags; first cut at IFD …
13:14 Changeset [3231] by curtis
Generator now distinguishes between multiple Images vs multiple Pixels.
13:05 Changeset [3230] by melissa
Fixed width/height mismatch detection, TiffData scrambling in single-file …
11:54 Changeset [3229] by curtis
OME-TIFF sample data generator now writes OME-TIFF with multiple series. …
10:51 Changeset [3228] by curtis
Progress on OME-TIFF sample file generator. Currently generates plain …
10:09 Changeset [3227] by melissa
Fixed min TiffData calculation.
09:50 Changeset [3226] by melissa
Look for the smallest TiffData tag, instead of always using the first one.

10/04/07:

14:58 Changeset [3225] by melissa
Multi-series OME-TIFF files should now work.

10/03/07:

16:35 Changeset [3224] by curtis
Begin work on utility for generating OME-TIFF sample datasets.
16:31 Changeset [3223] by curtis
Gray out time slider when no format reader is specified.
15:58 Changeset [3222] by curtis
Allow null IFormatReader, and add corresponding setImages signature.
11:47 Changeset [3221] by melissa
Only group files if the Image LSID is present, and print warnings if the …

10/02/07:

13:03 Changeset [3220] by melissa
Added support for MS Video 1 codec.
11:03 Changeset [3219] by melissa
Fixed how files are grouped.
10:29 Changeset [3218] by curtis
Allow processing from stdin.
10:12 Changeset [3217] by curtis
Whitespace.
08:13 Changeset [3216] by melissa
Set metadataComplete flag.

10/01/07:

14:15 Changeset [3215] by melissa
2007 Oct 01 release of LOCI Tools
14:15 Changeset [3214] by melissa
2007 Oct 01 release of LOCI Tools
14:15 Changeset [3213] by melissa
2007 Oct 01 release of LOCI Tools
14:15 Changeset [3212] by melissa
2007 Oct 01 release of LOCI Tools
14:15 Changeset [3211] by melissa
2007 Oct 01 release of LOCI Tools
14:15 Changeset [3210] by melissa
2007 Oct 01 release of LOCI Tools
14:15 Changeset [3209] by melissa
2007 Oct 01 release of LOCI Tools
14:15 Changeset [3208] by melissa
2007 Oct 01 release of LOCI Tools
14:10 Changeset [3207] by curtis
Clean up what's new list a bit for October 1 release.
13:55 Changeset [3206] by melissa
Updated what's new for next release.
12:34 Changeset [3205] by melissa
Don't create a StageLabel if all values are null.
11:49 Changeset [3204] by melissa
Removed obsolete 'valid bits' logic; minor cleanup/bugfixes.
11:46 Changeset [3203] by melissa
Don't autoscale images in the data browser.
11:22 Changeset [3202] by melissa
Added support for Photoshop PSD files.
10:28 Changeset [3201] by curtis
Miscellaneous tweaks.
10:28 Changeset [3200] by curtis
Fix some problems with XML validation.

09/28/07:

11:18 Changeset [3199] by curtis
Add hack to work around negative SizeZ/C/T values.
10:41 Changeset [3198] by melissa
Added support for uncompressed LIM files.

09/27/07:

14:42 Changeset [3197] by melissa
* Added isFalseColor() to IFormatReader API; updated ChannelFiller …
11:29 Changeset [3196] by melissa
Added option to turn off autoscaling.

09/26/07:

10:52 Changeset [3195] by melissa
Fixed NPE in get*BitLookupTable().
10:46 Changeset [3194] by curtis
Add printout of indexed color and LUT information to showinf.
10:33 Changeset [3193] by curtis
Print series names in core metadata listing if metadata store is set.
10:32 Changeset [3192] by curtis
Comment out unnecessary imports.

09/21/07:

11:13 Changeset [3191] by melissa
Slight speed improvement when reading intensity data.
10:07 Ticket #168 (LegacyQTWriter is broken) closed by melissa
fixed: Fixed in r3190.
10:07 Changeset [3190] by melissa
Fixed ClassCastException.
09:12 Changeset [3189] by melissa
Added support for JPEG and RLE-compressed DICOM images.

09/20/07:

13:23 Changeset [3188] by melissa
Added hack to compute emission/excitation wavelengths from channel name.

09/19/07:

14:57 Changeset [3187] by curtis
Comment out File menu for now.
14:54 Changeset [3186] by curtis
Use AWT menu bar instead of Swing menu bar to avoid Java3D heavyweight …
14:09 Changeset [3185] by curtis
Whitespace.
14:08 Changeset [3184] by curtis
Eliminate jikes warnings.
14:04 Changeset [3183] by curtis
Fix typo in javadoc.
14:00 Changeset [3182] by curtis
Add missing source code links to javadoc.
13:57 Changeset [3181] by curtis
Add ability to save and restore display projections from system clipboard.
13:33 Changeset [3180] by melissa
Added indexed color -> RGB option to ImageInfo; modified …
12:58 Ticket #166 (LegacyQTReader is broken) closed by melissa
fixed: Fixed in r3179. Rewriting LegacyQTReader was not necessary, as this was …
12:56 Changeset [3179] by melissa
Fixed close() bug.
12:03 Changeset [3178] by melissa
Added utility methods and reader wrapper to expand indexed color images.
10:55 Changeset [3177] by melissa
Added option to reorder stack.

09/18/07:

14:35 Changeset [3176] by melissa
Consolidated openImage implementations - haven't tested this on all …
13:41 Changeset [3175] by melissa
Added convenience method for calling setPixels(...) on a MetadataStore.
13:24 Changeset [3174] by melissa
Fixed strip offset calculation for IFDs that are missing strip byte …
12:15 Changeset [3173] by melissa
Fixed bug with getEffectiveSizeC() > 1 and getRGBChannelCount() > 1.
11:15 Changeset [3172] by melissa
Added isIndexed to macro functions.
10:45 Changeset [3171] by melissa
Make sure to set the appropriate series after calling setId.
09:46 Changeset [3170] by melissa
Fixed how RGB images are handled; added support for indexed color.

09/17/07:

16:27 Changeset [3169] by curtis
Update code to use most recent API.
16:16 Changeset [3168] by curtis
Update OME-TIFF conversion program to use most current API.
16:00 Changeset [3167] by curtis
Deal with exceptions from TiffTools.overwriteComment.
15:53 Changeset [3166] by curtis
Use simpler overwriteComment instead of overwriteIFDValue.
15:32 Changeset [3165] by curtis
Update Javadocs.
15:25 Changeset [3164] by curtis
Fix Javadoc links.
15:20 Changeset [3163] by curtis
Export should use tab-delineated, not space-separated, values.
10:45 Changeset [3162] by melissa
Minor bugfixes.

09/14/07:

09:56 Changeset [3161] by melissa
Fixed pixel type detection and offset calculation for zlib-compressed …
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